[phenixbb] phenix.real_space_refine
Pavel Afonine
pafonine at lbl.gov
Mon Oct 24 13:51:43 PDT 2016
On 10/24/16 23:50, Pavel Afonine wrote:
> I think "weight=1" may be a troublemaker.. It may be too far from
> what's optimal (that program determines by default if you don't
> specify any weight) and that may result in clashes that happen during
> refinement. Of course, something else may cause this as well.
>
> Pavel
>
> On 10/24/16 20:07, Oleg Sobolev wrote:
>> Hi Julia,
>>
>> In addition to Dorothee's response to your another e-mail, I would
>> indeed recommend check the model geometry, in particular, bad atomic
>> clashes (where 2 atoms are very close to each other). You can find
>> them in the .geo file which should be created by this point or in
>> log, under "Nonbonded interactions:". The worst clashes will be the
>> first in the list.
>>
>> Best regards,
>> Oleg Sobolev.
>>
>> On Mon, Oct 24, 2016 at 3:19 AM, Flis, Julia <julia.flis at charite.de
>> <mailto:julia.flis at charite.de>> wrote:
>>
>> Hello,
>>
>> my question is about the Phenix real space refinement. I am using
>> the Phenix version phenix-1.11-2563.
>>
>> My command looks as follows:
>> phenix.real_space_refine secondary_structure.enable=true
>> Model.pdb VOL.map elbow.Model_pdb.001.cif Model.pdb_ss.eff
>> resolution=3.8 weight=1
>>
>> My problem is that the refinement suddenly stops during the first
>> refinement cycle:
>>
>>
>>
>> Model_real_space_refined.log says:
>>
>> ********************** REFINEMENT MACRO_CYCLE 1 OF 5
>> *************************
>> -------------------------------------------------------------------------------
>> Update NCS operators
>> ********************
>> -------------------------------------------------------------------------------
>> Update rotamer restraints
>> *************************
>> -------------------------------------------------------------------------------
>> Global refinement
>> *****************
>> END
>>
>>
>> In the shell I get this :
>>
>> [...]
>> distance: 184426 - 184921: 3.388
>> distance: 184428 - 184920: 3.342
>> distance: 184448 - 184898: 3.373
>> distance: 184449 - 184897: 3.187
>> distance: 184491 - 184860: 3.066
>> distance: 184531 - 184770: 3.203
>> distance: 184554 - 184746: 3.137
>>
>> then it stops and the only files generated are
>> Model_real_space_refined.log and Model_initial.geo.
>>
>> Could you give me an advise? I have no clue what the problem
>> could be.
>>
>> Thank you,
>>
>> Julia
>>
>>
>
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